Do you think it should be more of a bonus to buy higher tier ships and less of a bonus to upgrade existing ones? I’m not fully versed on this game yet, this is just my initial observation.
I think your observation has been commented enough, however, to answer your question in theory, I might want to say: if every ship would be better in Synergy 1, than a previous ship with higher synergy, all ships would grow completely linearly, and therefore, playing any ship below the highest possible rank would be a waste of time.
While the current mechanism is for sure not perfect, I think it is fine as it is, however, in a more ideal scenario for my tastes, I would even say, that all tiers should be balanced completely in itself, meaning early ships get as strong as the highest rank in their tier, but need longer to level up; while different models of the same ship in the tier would act as specialization of the role; so it would actually be even more drastic in my ideal scenario, because a new rank 3 ship would be completely underpowered to a fully synergized and fitted rank 1 ship.
It would be then a design decision, if you make e.g. the earliest ship in each tier the one which makes it the most “variable” one, while the higher ranks would have presets to make them very “specialized”.
But it would be even more opposite to your assumption; you are therefore half served, since even if the next ranked ship begins weaker, usually, if you fully synergize it, it becomes a lot stronger, than the previous one - but it also depends on how you can actually fit the ship and use it, so sometimes this rule does not apply (e.g. many prefer a grey falcon (13) over a falcon-m (15))
Also, note, that while you move through a tier, you also spend money for modules, which might be better as you reach the highest of the tiered ships, so you can start them with better modules already. E.g. that is why in tiers like T3, where stability becomes crucial, having one purple voltage regulator you put in your new ships if they have a cap slot, can be a good investment; so generally, it is wise to keep some time with your ships, and later on think about what a lower ranked ship in the tier you play in can do, what the higher one cannot, and build a specific fit for it.
Just because you have finished synergizing a ship, does not mean, you cannot learn anything from it, or enjoy it how it is “supposed to be played” - even if while you are busy synergizing, this might be luxury.
With the current mechanism, usually the middle and upper rank of a tier are the most important ones (2,3,5,6,8,9,11,12, …), however this is just a general rule, since the implants, and amount of slots for modules change also a lot about the system. But others have clarified that already.